The board in charge of enforcing the Clean Water Act has written hundreds of permits and issued more than $30 million in penalties since 1985.

But the goals of the law - under which virtually every stream in San Joaquin County is considered polluted - remain unrealized after four decades.

The Central Valley Regional Water Quality Control Board regulates polluters up and down the Valley, from large city treatment plants such as Stockton's, to smaller industrial facilities.

Violations are common. Eighty-four percent of the larger facilities reported at least one violation in 2010.

The water board issues far more warnings than fines.

"We have gone straight to penalties, but in general we tend to like to do the more progressive enforcement," said Pamela Creedon, the board's executive officer.

At least one critic calls for more aggressive oversight, looking at facts such as these:

» The board sent 210 notices of violation in 2010, while issuing 13 penalties;

» Fewer than half of the self-monitoring reports submitted by polluters were actually reviewed in 2010;

» The board inspected 76 percent of the major facilities but just 6 percent of the smaller "minor" facilities in 2010; and

» If penalties are issued, in some cases polluters can apply fines to environmental projects that help return them to compliance.

Bill Jennings, a Stockton environmentalist whose California Sportfishing Protection Alliance often clashes with the board, said this creates a "pay to pollute" system.

"The board enforces the Clean Water Act like the Highway Patrol enforces the speed laws between here and Sacramento," Jennings said. "If you drive the speed limit you will be the slowest car on the highway."

Staffing is a challenge, the water board's Creedon said.

Lack of personnel makes it harder to renew permits in a timely manner - meaning some polluters continue to operate under older, less stringent rules.

Plans required under the Clean Water Act to remove rivers and streams from the list of polluted waterways have in some cases not been written or are not being aggressively implemented. And some rivers and streams have still not been tested to even determine the scope of the problem.

"We keep trying," Creedon said. "In the age of budget cuts it's difficult. We've been losing resources and staffing, but we're doing a good job."

The Environmental Protection Agency issued an action plan this year calling Clean Water Act programs "not adequate" for protecting the Delta.

But those programs alone won't get the job done, said Karen Schwinn, associate director of EPA's water division in San Francisco. She defended the regional board's progress.

"Most of the flow of the San Joaquin River, about 90 percent, is taken off upstream, and the landscape of the Valley has been enormously changed," Schwinn said. "Whether good or bad, it has impacted water quality. Those are things difficult, if not impossible, to get at with traditional Clean Water Act tools."

The Clean Water Act's list of polluted waterways reflects only the roughly 200 chemicals regulated by the law. About 100,000 chemicals have been approved for use since 1980.

"These things are being synthesized at a pace where it's really hard to keep up," said James Cloern, an aquatic ecologist with the U.S. Geological Survey.

These chemicals escape through treatment plants in minute concentrations - sometimes as small as 1 drop for every trillion drops of water.

They may not be lethal. But they may be harming species' ability to reproduce, a long-term threat to their viability.

Susanne Brander, a former University of California, Davis, doctoral student, spent two years studying fish downstream from a wastewater treatment plant in the Suisun Marsh, west of the Delta.

She discovered the sex ratio for this population of fish, known as Mississippi silverside, had been "skewed male - significantly male." Instead of about 50/50, the gender ratio was 70/30.

"We don't necessarily know why," Brander said.

A good suspect are pyrethroids, newer pesticides considered safer than their predecessors but are believed to alter reproductive systems. Pyrethroids have been detected in urban waterways in the Delta.

"You'd be surprised how many people dump extra pesticides down the drain to dispose of them," Brander said.

Overall, water quality has improved the past 40 years, she said, but the effects of newer chemicals often aren't known until they're on the market.

"We're always reacting," she said.

Ultimately, water quality is not a wonky subject for scientists and fish biologists. It affects everyone in Stockton, whether you drink the water, swim in the Delta, eat striped bass or salmon, or merely enjoy the aesthetics of living in a waterfront home.

"I think there's been tremendous benefits for people in the past 40 years," said Dan Odenweller, a former member of the water board who lives in Stockton.

"We do still have waters unsafe for contact sports," he said. "When I was on the county's dive rescue team, we were seriously looking at dry suits to avoid contact with water because of the lesions and parasites people were picking up. But it's all relative - I know people who do waterskiing and don't think anything of it."

Dale Sanders, an environmental educator and advocate for the Calaveras River, seems more pessimistic. He was leading a group of schoolchildren to the river last spring when they came across an all-too-familiar sign warning about water quality. A toxic spill had occurred upstream.

"We have fouled our own nest," he said later. "The death knell of any species is, if it pollutes itself out of existence, it's a goner. Unless we raise a bunch of kids smarter than we are, we're going to go down the tubes pretty quick."

Fisherman John Banks, 77, grew up in Stockton. On hot summer days he and his buddies would ride their bikes down to Dad's Point to splash around in the Deep Water Channel (the swimming pool at Stribley Park was for sissies, he said).

When they were thirsty, they simply took a drink from the river.

That was before the Clean Water Act, but it was also before the state and federal government started pumping Delta water as far south as San Diego. Banks believes the rivers remain polluted today primarily because of the loss of that water.

Most people in Stockton don't understand the river Banks remembers – “my river,” he calls it.

“They can't imagine a sparkling river flowing through a major metropolis,” Banks said. “That's completely beyond their understanding.